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Detailed information for vg1113356571:

Variant ID: vg1113356571 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 13356571
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACACGAACAGCTCCAAACTCTTTGTGTAACCCTGCCATAGTGAGTAGCAAACAAGAAACATATACAAGAATATATACGTTCCTATCAACTACTAGGTAG[T/C]
GGAAGCTCACAAATCACACACACTCAAGCTTTACATCGAGCTCTTACAAGTTCTTACCAATGCAAGCGGAATGGTGACATACACCGACTCAACCAAGCAC

Reverse complement sequence

GTGCTTGGTTGAGTCGGTGTATGTCACCATTCCGCTTGCATTGGTAAGAACTTGTAAGAGCTCGATGTAAAGCTTGAGTGTGTGTGATTTGTGAGCTTCC[A/G]
CTACCTAGTAGTTGATAGGAACGTATATATTCTTGTATATGTTTCTTGTTTGCTACTCACTATGGCAGGGTTACACAAAGAGTTTGGAGCTGTTCGTGTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.60%	6.20%	13.25%	3.91%	NA
All Indica	2759	61.10%	10.50%	22.15%	6.27%	NA
All Japonica	1512	99.10%	0.10%	0.40%	0.33%	NA
Aus	269	99.30%	0.40%	0.37%	0.00%	NA
Indica I	595	57.60%	25.70%	15.13%	1.51%	NA
Indica II	465	60.00%	3.70%	16.13%	20.22%	NA
Indica III	913	64.20%	5.30%	29.79%	0.77%	NA
Indica Intermediate	786	60.70%	9.20%	22.14%	8.02%	NA
Temperate Japonica	767	98.60%	0.10%	0.65%	0.65%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	84.40%	0.00%	7.78%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1113356571	T -> DEL	N	N	silent_mutation	Average:27.675; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg1113356571	T -> C	LOC_Os11g23210.1	downstream_gene_variant ; 4950.0bp to feature; MODIFIER	silent_mutation	Average:27.675; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg1113356571	T -> C	LOC_Os11g23200.1	intron_variant ; MODIFIER	silent_mutation	Average:27.675; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1113356571	NA	9.38E-08	mr1308_2	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1113356571	NA	3.00E-07	mr1361_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251